Dear Jim Kress and Li Zhen,
Thank you very much for your answers.
In the last test I mistakenly used the wrong filename.
I corrected the file name and pdb4amber completed without errors.
Li's advice to use the --reduce parameter helps to correct the initial error
I noticed this in my first report.
My apologies for my mistake in file name.
Michael
________________________________
From: James Kress via AMBER <amber.ambermd.org>
Sent: Thursday, July 11, 2024 10:00 PM
To: 'AMBER Mailing List' <amber.ambermd.org>
Subject: Re: [AMBER] AMBER24 error report when running pdb4amber command
Is this file in the directory you are using?
IQSEC2_w_free_reduced_nh.pdb
The error message is explicit in that pdb4amber could not find that file.
Jim Kress
James Kress Ph.D., President
The KressWorks® Institute
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-----Original Message-----
From: Michael Shokhen via AMBER <amber.ambermd.org>
Sent: Thursday, July 11, 2024 2:31 PM
To: Li, Zhen <lizhen6.chemistry.msu.edu>
Cc: amber.ambermd.org
Subject: Re: [AMBER] AMBER24 error report when running pdb4amber command
Hi Li,
Thank you for your response.
Following your advise I used --reduce.
Unfortunately, it didn't help.
See below copy from terminal.
Michael
> pwd
/var/spool/scratch/shokhen/US4_Gln391_Gly_Gly_Ser627
> pdb4amber -i IQSEC2_w_free_reduced_nh.pdb -o
> IQSEC2_w_free_reduced.amber.pdb --dry --reduce
==================================================
Summary of pdb4amber for: IQSEC2_w_free_reduced_nh.pdb ===================================================
Traceback (most recent call last):
File "/var/spool/scratch/shokhen/amber24/bin/pdb4amber", line 33, in <module>
sys.exit(load_entry_point('pdb4amber==22.0', 'console_scripts', 'pdb4amber')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/pdb4amber/pdb4amber.py", line 819, in main
run(
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/pdb4amber/pdb4amber.py", line 516, in run
parm = parmed.read_PDB(pdbin)
^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/parmed/formats/pdb.py", line 422, in parse
fileobj = genopen(filename, 'r')
^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/parmed/utils/io.py", line 95, in genopen
return open(name, mode, encoding=DEFAULT_ENCODING)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'IQSEC2_w_free_reduced_nh.pdb'
>
________________________________
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Sent: Thursday, July 11, 2024 8:38 PM
To: Michael Shokhen <michael.shokhen.biu.ac.il>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: AMBER24 error report when running pdb4amber command
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Hi Michael,
Have you tried --reduce instead of -reduce?
From: Michael Shokhen via AMBER <amber.ambermd.org>
Date: Thursday, July 11, 2024 at 1:33 PM
To: AMBER.ambermd.org <amber.ambermd.org>
Subject: [AMBER] AMBER24 error report when running pdb4amber command
Dear AMBER experts,
I have installed on my server Amber24 and AmberTools24.
All four tests were completed without errors: test.serial, test.parallel, tcsh shell. test.cuda.serial, test.cuda.parallel.
I have on my sever Rocky Linux VERSION="8.10 (Green Obsidian)"; tcsh shell.
Unfortunately, I received an error report when running pdb4amber command. See copy from terminal below.
I need your advice how to resolve the problem.
Thank you,
Michael
/var/spool/scratch/shokhen/US4_Gln391_Gly_Gly_Ser627
> pdb4amber -i US4_Gly_Gly_nh.pdb -o US4_Gly_Gly_reduced.amber.pdb --dry
> –reduce
==================================================
Summary of pdb4amber for: –reduce
===================================================
Traceback (most recent call last):
File "/var/spool/scratch/shokhen/amber24/bin/pdb4amber", line 33, in <module>
sys.exit(load_entry_point('pdb4amber==22.0', 'console_scripts', 'pdb4amber')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/pdb4amber/pdb4amber.py", line 819, in main
run(
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/pdb4amber/pdb4amber.py", line 516, in run
parm = parmed.read_PDB(pdbin)
^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/parmed/formats/pdb.py", line 422, in parse
fileobj = genopen(filename, 'r')
^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/parmed/utils/io.py", line 95, in genopen
return open(name, mode, encoding=DEFAULT_ENCODING)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '–reduce'
>
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Received on Thu Jul 11 2024 - 12:30:02 PDT
